GrantRVD/data-neuroscience

Publications & Papers

GrantRVD opened this issue · 3 comments

GrantRVD commented

While any kind of neuroscientific data has good potential as a learning tool when paired with the right tutorials, it would be ideal to use data associated with peer-reviewed publications. Ideally, each sub-domain of neuroscience should have five or so

Contributors: Please reply to this issue with your suggestions for papers and publications along with a brief elaboration on what concepts or skills a user would acquire by reading and re-performing the analyses done in the paper. Keep in mind the following requirements:

  • There must be a legal way to access the paper for free. To satisfy this requirement, the paper may be

    • open-access
    • available on one of the authors' websites in a nearly identical form
    • available through another legal tool, like Unpaywall or Open Access Button

  • The data used for the paper must be available for use, ideally small enough to fit on a consumer harddrive

  • The principal analyses of the paper should be, at least theoretically, reproducible with freely available software and programming tools (e.g. Python, R, Julia, etc.)

If you're unsure that a paper meets the above requirements or think it's worth mentioning anyway, you're welcome to post it and we'll discuss if and how it can be included in the syllabus.

npscience commented

Note to self - contribute here

Initial thoughts:
See work from Janelia Farm (Karel Svoboda, Albert Cardona, Jeremy Freeman labs - just search their names from the eLife search bar elifesciences.org) published with eLife. They often include Jupyter notebooks and link to github repos with their data and code. Jeremy Freeman also developed Binder to wrap up data and code into Docker for reproducible computation by anyone else.

npscience commented

Check out https://elifesciences.org/subjects/neuroscience

And also see if our XML dump or API are useful for searching for things: https://elifesciences.org/inside-elife/6933fe8e/resources-for-developers

GrantRVD commented

Thanks, @npscience! I've met Jeremy several times and visited HHMI in person, so I know they're very much on the edge of doing good, reproducible experiments and their material will make ideal components of the syllabus. I've even got binder mentioned on #1 as a potential future addition, once sufficient resources have been collected. Incidentally, I just copied the resources for developers link into one of the other issues here, before I saw your replies.